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Exploring the manganese-dependent interaction between a transcription factor and its corresponding DNA: insights from gas-phase electrophoresis on a nES GEMMA instrument

Leščić Ašler, Ivana; Radman, Katarina; Jelić Matošević, Zoe; Bertoša, Branimir; Weiss, Victor U.; Marchetti-Deschmann, Martina (2024) Exploring the manganese-dependent interaction between a transcription factor and its corresponding DNA: insights from gas-phase electrophoresis on a nES GEMMA instrument. Analytical and Bioanalytical Chemistry, 416 (24). pp. 5377-5386. ISSN 1618-2642

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Abstract

Manganese ion homeostasis is vital for bacteria and is achieved via manganese-dependent transcription factors. Manganese mediation of transcription factor attachment to the corresponding oligonucleotide sequences can be investigated, e.g. via electrophoretic mobility shift assays (EMSA). Formation of specific biocomplexes leads to differences in the migration pattern upon gel electrophoresis. Focusing on electrophoresis in the gas-phase, applying a nano electrospray gas-phase electrophoretic mobility molecular analyzer (nES GEMMA) also known as nES differential mobility analyzer (nES DMA), and on transcription factors (MntR proteins) from Bacillus subtilis and Mycobacterium tuberculosis, we took interest in the gas-phase electrophoresis of the corresponding biospecific complexes. We compared nES GEMMA, separating analytes in the nanometer regime (a few to several hundred nm in diameter) in the gas-phase in their native state according to particle size, to EMSA data. Indeed we were able to demonstrate manganese-mediated attachment of MntR to target genomic sequences with both analytical techniques. Despite some inherent pitfalls of the nES GEMMA method like analyte/instrument surface interactions, we were able to detect the target complexes. Moreover, we were able to calculate the molecular weight (MW) of the obtained species by application of a correlation function based on nES GEMMA obtained data. As gas-phase electrophoresis also offers the possibility of offline hyphenation to orthogonal analysis techniques, we are confident that nES GEMMA measurements are not just complementary to EMSA, but will offer the possibility of further in-depth characterization of biocomplexes in the future.

Item Type: Article
Uncontrolled Keywords: protein-DNA binding; nES GEMMA; transcriptional factors
Subjects: NATURAL SCIENCES > Chemistry > Analytic Chemistry
NATURAL SCIENCES > Biology > Biochemistry and Molecular Biology
Divisions: Division of Physical Chemistry
Projects:
Project titleProject leaderProject codeProject type
Manganovi metalosenzori-MaMesBranimir BertošaIP-2020-02-3446HRZZ
Depositing User: Lorena Palameta
Date Deposited: 29 Oct 2024 13:53
URI: http://fulir.irb.hr/id/eprint/9223
DOI: 10.1007/s00216-024-05473-9

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